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koushiksarker
 Post subject: docking not possible
PostPosted: Wed Mar 14, 2012 5:24 pm 
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is there any message shown by autodock if atall ligand doesnot bind with receptor.
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Ruth Huey
 Post subject: Re: docking not possible
PostPosted: Tue Mar 27, 2012 5:02 pm 
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In your docking log file ('dlg') look at the sections for each run which begin:
'DOCKED: USER Estimated Free Energy of Binding' .
How well the ligand binds with the receptor is the "Final Intermolecular Energy" .

These 'intermolecular energies' for a ligand which does not bind at all with the receptor will all be close to zero or even positive...
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